iMeta最新文献

{"title":"BioLadder: A bioinformatic platform primarily focused on proteomic data analysis","authors":"Yupeng Zhang,&nbsp;Chunyuan Yang,&nbsp;Jinhao Wang,&nbsp;Lixin Wang,&nbsp;Yan Zhao,&nbsp;Longqing Sun,&nbsp;Wei Sun,&nbsp;Yunping Zhu,&nbsp;Jingli Li,&nbsp;Songfeng Wu","doi":"10.1002/imt2.215","DOIUrl":"https://doi.org/10.1002/imt2.215","url":null,"abstract":"<p>BioLadder (https://www.bioladder.cn/) is an online data analysis platform designed for proteomics research, which includes three classes of experimental data analysis modules and four classes of common data analysis modules. It allows for a variety of proteomics analyses to be conducted easily and efficiently. Additionally, most modules can also be utilized for the analysis of other omics data. To facilitate user experience, we have carefully designed four different kinds of functions for customers to quickly and accurately utilize the relevant analysis modules.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.215","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141967021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep learning enhancing guide RNA design for CRISPR/Cas12a-based diagnostics","authors":"Baicheng Huang,&nbsp;Ling Guo,&nbsp;Hang Yin,&nbsp;Yue Wu,&nbsp;Zihan Zeng,&nbsp;Sujie Xu,&nbsp;Yufeng Lou,&nbsp;Zhimin Ai,&nbsp;Weiqiang Zhang,&nbsp;Xingchi Kan,&nbsp;Qian Yu,&nbsp;Shimin Du,&nbsp;Chao Li,&nbsp;Lina Wu,&nbsp;Xingxu Huang,&nbsp;Shengqi Wang,&nbsp;Xinjie Wang","doi":"10.1002/imt2.214","DOIUrl":"10.1002/imt2.214","url":null,"abstract":"<p>Rapid and accurate diagnostic tests are fundamental for improving patient outcomes and combating infectious diseases. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas12a-based detection system has emerged as a promising solution for on-site nucleic acid testing. Nonetheless, the effective design of CRISPR RNA (crRNA) for Cas12a-based detection remains challenging and time-consuming. In this study, we propose an enhanced crRNA design system with deep learning for Cas12a-mediated diagnostics, referred to as EasyDesign. This system employs an optimized convolutional neural network (CNN) prediction model, trained on a comprehensive data set comprising 11,496 experimentally validated Cas12a-based detection cases, encompassing a wide spectrum of prevalent pathogens, achieving Spearman's <i>ρ</i> = 0.812. We further assessed the model performance in crRNA design for four pathogens not included in the training data: Monkeypox Virus, Enterovirus 71, Coxsackievirus A16, and <i>Listeria monocytogenes</i>. The results demonstrated superior prediction performance compared to the traditional experiment screening. Furthermore, we have developed an interactive web server (https://crispr.zhejianglab.com/) that integrates EasyDesign with recombinase polymerase amplification (RPA) primer design, enhancing user accessibility. Through this web-based platform, we successfully designed optimal Cas12a crRNAs for six human papillomavirus (HPV) subtypes. Remarkably, all the top five predicted crRNAs for each HPV subtype exhibited robust fluorescent signals in CRISPR assays, thereby suggesting that the platform could effectively facilitate clinical sample testing. In conclusion, EasyDesign offers a rapid and reliable solution for crRNA design in Cas12a-based detection, which could serve as a valuable tool for clinical diagnostics and research applications.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.214","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141336521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A universal oral microbiome-based signature for periodontitis","authors":"Mingyan Geng,&nbsp;Min Li,&nbsp;Yun Li,&nbsp;Jiaying Zhu,&nbsp;Chuqing Sun,&nbsp;Yan Wang,&nbsp;Wei-Hua Chen","doi":"10.1002/imt2.212","DOIUrl":"10.1002/imt2.212","url":null,"abstract":"<p>We analyzed eight oral microbiota shotgun metagenomic sequencing cohorts from five countries and three continents, identifying 54 species biomarkers and 26 metabolic biomarkers consistently altered in health and disease states across three or more cohorts. Additionally, machine learning models based on taxonomic profiles achieved high accuracy in distinguishing periodontitis patients from controls (internal and external areas under the receiver operating characteristic curves of 0.86 and 0.85, respectively). These results support metagenome-based diagnosis of periodontitis and provide a foundation for further research and effective treatment strategies.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.212","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141352263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"JCVI: A versatile toolkit for comparative genomics analysis","authors":"Haibao Tang,&nbsp;Vivek Krishnakumar,&nbsp;Xiaofei Zeng,&nbsp;Zhougeng Xu,&nbsp;Adam Taranto,&nbsp;Johnathan S. Lomas,&nbsp;Yixing Zhang,&nbsp;Yumin Huang,&nbsp;Yibin Wang,&nbsp;Won Cheol Yim,&nbsp;Jisen Zhang,&nbsp;Xingtan Zhang","doi":"10.1002/imt2.211","DOIUrl":"10.1002/imt2.211","url":null,"abstract":"<p>The life cycle of genome builds spans interlocking pillars of assembly, annotation, and comparative genomics to drive biological insights. While tools exist to address each pillar separately, there is a growing need for tools to integrate different pillars of a genome project holistically. For example, comparative approaches can provide quality control of assembly or annotation; genome assembly, in turn, can help to identify artifacts that may complicate the interpretation of genome comparisons. The JCVI library is a versatile Python-based library that offers a suite of tools that excel across these pillars. Featuring a modular design, the JCVI library provides high-level utilities for tasks such as format parsing, graphics generation, and manipulation of genome assemblies and annotations. Supporting genomics algorithms like MCscan and ALLMAPS are widely employed in building genome releases, producing publication-ready figures for quality assessment and evolutionary inference. Developed and maintained collaboratively, the JCVI library emphasizes quality and reusability.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.211","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141354097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The challenge and opportunity of gut microbiota-targeted nanomedicine for colorectal cancer therapy","authors":"Yaohua Wei,&nbsp;Feng Shen,&nbsp;Huidong Song,&nbsp;Ruifang Zhao,&nbsp;Weiyue Feng,&nbsp;Yue Pan,&nbsp;Xiaobo Li,&nbsp;Huanling Yu,&nbsp;Giuseppe Familiari,&nbsp;Michela Relucenti,&nbsp;Michael Aschner,&nbsp;Hanping Shi,&nbsp;Rui Chen,&nbsp;Guangjun Nie,&nbsp;Hanqing Chen","doi":"10.1002/imt2.213","DOIUrl":"10.1002/imt2.213","url":null,"abstract":"<p>The gut microbiota is an integral component of the colorectal cancer (CRC) microenvironment and is intimately associated with CRC initiation, progression, and therapeutic outcomes. We reviewed recent advancements in utilizing nanotechnology for modulating gut microbiota, discussing strategies and the mechanisms underlying their design. For future nanomedicine design, we propose a 5I principle for individualized nanomedicine in CRC management.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.213","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141363691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ms gene and Mr gene: Microbial-mediated spatiotemporal communication between plants","authors":"Ming-Hao Lv,&nbsp;Wen-Chong Shi,&nbsp;Ming-Cong Li,&nbsp;Bo Zhou,&nbsp;Yong-Xin Liu,&nbsp;Zheng Gao","doi":"10.1002/imt2.210","DOIUrl":"10.1002/imt2.210","url":null,"abstract":"<p>Within dynamic agroecosystems, microbes can act as key intermediaries, facilitating spatiotemporal communication among plants. Future research could categorize key plant genes involved in plant–microbe interactions into microbiome-shaping genes (Ms genes) and microbiome-responsive genes (Mr genes), potentially leading to the construction of spatiotemporal molecular networks with microbes as intermediaries.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.210","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141375090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Robust CRISPR/Mb2Cas12a genome editing tools in cotton plants","authors":"Fengjiao Hui,&nbsp;Xu Tang,&nbsp;Bo Li,&nbsp;Muna Alariqi,&nbsp;Zhongping Xu,&nbsp;Qingying Meng,&nbsp;Yongxue Hu,&nbsp;Guanying Wang,&nbsp;Yong Zhang,&nbsp;Xianlong Zhang,&nbsp;Shuangxia Jin","doi":"10.1002/imt2.209","DOIUrl":"10.1002/imt2.209","url":null,"abstract":"<p>The efficiency and accuracy of the CRISPR/Mb2Cas12a system were demonstrated in cotton, achieving an efficiency of over 90% at target sites. Notably, Mb2Cas12a exhibited significant tolerance under different temperatures ranging from 22°C to 32°C. Additionally, the Mb2Cas12a system revealed effective editing at more relaxed VTTV PAM sites in the cotton genome, which expanded the genome editing range by approximately 2.6-fold than the wide-type LbCas12a. Finally, a multiplex genome editing system was also developed based on Mb2Cas12a, enabling simultaneous editing of eight target sites using a single crRNA cassette.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.209","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141267050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The feasibility of using pathobiome strains as live biotherapeutic products for human use","authors":"Pengfei Jin,&nbsp;Xiong Lin,&nbsp;Wenfeng Xu,&nbsp;Kangning Li,&nbsp;Xiaoxiao Zhao,&nbsp;Sirui Guo,&nbsp;Zinan Zhao,&nbsp;Lujie Jiang,&nbsp;Feng Liao,&nbsp;Longgang Chang,&nbsp;Min Wang,&nbsp;Yanmin Liu,&nbsp;Shaolei Huang,&nbsp;Zhangran Chen,&nbsp;Fusui Ji","doi":"10.1002/imt2.202","DOIUrl":"https://doi.org/10.1002/imt2.202","url":null,"abstract":"<p>The evaluation of pathobiome strains should be conducted at the strain level, involving the identification of the functional genes, while considering the impact of ecological niche and drug interactions. The safety, efficacy, and quality management of live biotherapeutic products (LBPs), especially pathobiome strains, have certain peculiarities. Promising development methods include the recombinant LBP and active metabolites.\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.202","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MASH-Ocean 1.0: Interactive platform for investigating microbial diversity, function, and biogeography with marine metagenomic data","authors":"Yinzhao Wang,&nbsp;Liuyang Li,&nbsp;Qiang Li,&nbsp;Yaoxun Hu,&nbsp;Wenjie Li,&nbsp;Zhile Wu,&nbsp;Hungchia Huang,&nbsp;Zhenbo Lv,&nbsp;Wan Liu,&nbsp;Ruifang Cao,&nbsp;Guoping Zhao,&nbsp;Fengping Wang,&nbsp;Guoqing Zhang","doi":"10.1002/imt2.201","DOIUrl":"10.1002/imt2.201","url":null,"abstract":"<p>A large number of oceanic metagenomic data and environmental metadata have been published. However, most studies focused on limited ecosystems using different analysis tools, making it challenging to integrate these data into robust results and comprehensive global understanding of marine microbiome. Here, we constructed a systematic and quantitative analysis platform, the Microbiome Atlas/Sino-Hydrosphere for Ocean Ecosystem (MASH-Ocean: https://www.biosino.org/mash-ocean/), by integrating global marine metagenomic data and a unified data processing flow. MASH-Ocean 1.0 comprises 2147 metagenomic samples with five analysis modules: sample view, diversity, function, biogeography, and interaction network. This platform provides convenient and stable support for researchers in microbiology, environmental science, and biogeochemistry, to ensure the integration of omics data generated from hydrosphere ecosystems, to bridge the gap between elusive omics data and biological, ecological, and geological discovery, ultimately to foster the formation of a comprehensive atlas for aquatic environments.\u0000\u0000 <figure>\u0000 <div><picture>\u0000 <source></source></picture><p></p>\u0000 </div>\u0000 </figure></p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.201","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141123596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition","authors":"Lingyan Ma,&nbsp;Wentao Lyu,&nbsp;Tao Zeng,&nbsp;Wen Wang,&nbsp;Qu Chen,&nbsp;Jiangchao Zhao,&nbsp;Guolong Zhang,&nbsp;Lizhi Lu,&nbsp;Hua Yang,&nbsp;Yingping Xiao","doi":"10.1002/imt2.198","DOIUrl":"10.1002/imt2.198","url":null,"abstract":"<p>The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome-assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region-specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic-resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production.</p>","PeriodicalId":73342,"journal":{"name":"iMeta","volume":"3 4","pages":""},"PeriodicalIF":23.7,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/imt2.198","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140978338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}